Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,840,646	0	T	C	51.5%	12.5 / 38.4	33	D365G (GAT→GGT)	nepI	putative transporter
Reads supporting (aligned to +/- strand):  ref base T (9/7);  new base C (0/17);  total (9/24)
Fisher's exact test for biased strand distribution p-value = 2.97e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.60e-03

CCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATGCAAAAGTTAGCC  >  NC_000913/3840496‑3840793                                                                                                                                                        |                                                                                                                                                    cccGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAAtattat                                                                                                                                                     >  1:153750/1‑151 (MQ=255)     gATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCCCCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAg                                                                                                                                                 <  1:524710/151‑1 (MQ=255)                 cAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAAccgcc                                                                                                                                     <  2:103193/151‑1 (MQ=255)                                        ttcttTACCTAATATAAGGATTTCTTCATTTTCCCCTTTGCAGAAACCAACAATGCAGTCAGCACCATAAATGTGCC‑GAACAACATCAACGGCGAATTCAGACCAATTTTACCCAGCGAAAAACCGCCGATTGCCGCGCCACAGGTAt                                                                                                                 <  1:197168/148‑1 (MQ=255)                                           tttCCCTGATATCAGGTTTTCTTCATTTCCCCTTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCC‑GAACAACATCAACGGCGAAGTCAGACCAATATTACCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGc                                                                                                             <  1:315098/149‑1 (MQ=255)                                           tttACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATAAATGTGCC‑GGACAACATCAACGGCGAAGTAAGACCAATATTACCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCa                                                                                                            <  1:315570/150‑1 (MQ=255)                                               ccTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAAGGCAGTCAGCAACATAAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTACCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTg                                                                                                       <  2:538282/151‑1 (MQ=255)                                                 tGATATCAGGTTTTCTTCATTTTCCCTTTTGCAGTACCCAACAATGCAGTCAGAAACATCAATGTCCC‑GGACAAAATAAGCGGGAAAGTCAGACCAATTTTATCCAGCGAAAAGCCGCCGATTGCCGCGCCACAGGTATTAGc                                                                                                             <  1:226379/143‑1 (MQ=255)                                                          gATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGcc                                                                                             >  2:597562/1‑150 (MQ=255)                                                            tttCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCAcc                                                                                          >  1:319743/1‑151 (MQ=255)                                                                  cATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAAt                                                                                     >  2:497626/1‑150 (MQ=255)                                                                       tCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGAccc                                                                               >  2:307942/1‑151 (MQ=255)                                                                          ccTTTCAAGTACCCAACAATGCAGTCACCACCACCAATGTCCC‑GGACAACATCAACGGCGACGTCAGCCAAATATTACCCGGCGCAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCgg                                                                             <  1:77251/150‑1 (MQ=255)                                                                                 agaaaCCAACAATGCAGTCAGCAACATCAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCt                                                                     <  1:68926/148‑1 (MQ=255)                                                                                 aGTAACCAACAATGCAGTCAGCAACATCAATGTGCC‑GAACAACATCACCGGCGAAGTCAGACAAATATTATCCAGCGCATAACCGCCGATTGCCGCACCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCttttt                                                                       <  2:323963/149‑1 (MQ=255)                                                                                    aacaaacaATGCAGTCAGAAACATCAATGTGCC‑GAACAACATCAACGGCAAAGTCAGACAAATATTACCCACCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCt                                                                     <  1:96626/148‑1 (MQ=255)                                                                                     aCCAACAAGGCAGTCAG‑AAAAACAAAGGGCCGGGAAAACACCACCGGCGAAGTCACACCAATATAACCCAGCGCAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCt                                                                 <  2:153799/151‑1 (MQ=255)                                                                                        aacaaTGCAGTCAGCAACATCAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGAt                                                              >  2:302269/1‑151 (MQ=255)                                                                                                        aCATCAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCATCGAGCGGGt                                              >  1:96784/1‑151 (MQ=255)                                                                                                            cAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATc                                          >  2:542244/1‑151 (MQ=255)                                                                                                             aaTGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATcc                                         >  1:447647/1‑151 (MQ=255)                                                                                                                        acaacaTCAACGGGGAAGTCAGCCAAATATTACCCAGCGCAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTCCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGa                                  <  1:506839/148‑1 (MQ=255)                                                                                                                          aacaTCAACGGCGAATTCAAACAAATATTACCCAGCGCAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAg                              <  1:608115/150‑1 (MQ=255)                                                                                                                           acaTCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGcc                            >  1:343431/1‑151 (MQ=255)                                                                                                                                aaCGGCGAAGTCAGACAAAAATTACCCAGCGAATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACgg                       <  1:542255/151‑1 (MQ=255)                                                                                                                                aaCGGCGAAGCCAGACCAATATTACCCAGCGAAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGa                          <  2:9205/148‑1 (MQ=255)                                                                                                                                   gggaaaGTCACCCCAATATTCCCGCGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGaa                    <  1:71707/147‑1 (MQ=255)                                                                                                                                       aaGTCAGACCAATATTACCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAAc                   <  1:539008/148‑1 (MQ=255)                                                                                                                                       aaGTCAGACAAATATTATCCAGCGAATACCCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCa                 <  2:278033/150‑1 (MQ=255)                                                                                                                                            acaCCAATATTACCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCa                 <  1:560181/143‑1 (MQ=255)                                                                                                                                              acaaaTATTACCCAGCGAAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATGCaaa          <  1:227785/147‑1 (MQ=255)                                                                                                                                                 aaTATTATCCAGCGCATACCCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATGCAAAAGt       <  2:600160/150‑1 (MQ=255)                                                                                                                                                 aaTATTACCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATGCAAAAGt       <  2:326747/150‑1 (MQ=255)                                                                                                                                                 aaTATTACCCAGCGAATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATGCAAAAg        <  2:343424/149‑1 (MQ=255)                                                                                                                                                     ttatCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATGCAAAAGTTAGcc  >  2:135845/1‑151 (MQ=255)                                                                                                                                                        |                                                                                                                                                    CCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCC‑GGACAACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATGCAAAAGTTAGCC  >  NC_000913/3840496‑3840793

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑